HHsearch alignment for GI: 254780351 and conserved domain: pfam04552
>pfam04552 Sigma54_DBD Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins.
Probab=90.80 E-value=0.78 Score=25.26 Aligned_cols=75 Identities=25% Similarity=0.194 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHH-H--CCCEE------EEECCCCCCEEEEEECHHHHH-HHHHHHHHHHHHHHHH
Q ss_conf 796889999985477105679999999-7--78878------863610071056445788999-9999999999999999
Q gi|254780351|r 69 LELTAGELRSRGYYLGSNVSYNLKKLI-D--LGFIK------HQRSRIDKRSIRISLTQSGKE-IAETISQLYQRHIESI 138 (171)
Q Consensus 69 ~~~t~~eLa~~l~i~~~tvs~~i~~Le-~--~G~i~------r~~~~~D~R~~~i~LT~~G~~-~~~~~~~~~~~~~~~l 138 (171)
T Consensus 48 ~PLtlk~iA~~l~lh~STVSRav~~Kyi~tp~Gi~~lk~fFs~~~~~-----------~~~~~~S~~~ik~~I~~lI~~E 116 (160)
T pfam04552 48 RPLTLREVAEALGMHESTVSRATTNKYLATPRGLFELKYFFSSAVST-----------SGGGEASATAIRALIKKLIAAE 116 (160)
T ss_pred CCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEEEHHHHHHCCCCC-----------CCCCCHHHHHHHHHHHHHHHHC
T ss_conf 57619999988099810699999613976799516599985013678-----------8863022999999999999824
Q ss_pred HHHCCCCHHHHHHHHH
Q ss_conf 8534999899999999
Q gi|254780351|r 139 DKVGGLSVDDFIAMNK 154 (171)
Q Consensus 139 ~~~~~ls~ee~~~l~~ 154 (171)
T Consensus 117 d~~~PlSD~~I~~~L~ 132 (160)
T pfam04552 117 DPKKPLSDDKIVELLK 132 (160)
T ss_pred CCCCCCCHHHHHHHHH
T ss_conf 7899999999999999